CHARMM Developer's Change Log
Entries in each node are recorded by CHARMM developers to indicate new
and modified features of CHARMM during the development cycle, i.e., the
alpha version period.
------------------------------------------------------
CHARMM22.0.b Release April 22, 1991
CHARMM22.0.b1 Release September 30, 1991
CHARMM22 Release January 1, 1992
c22g1 Release February 15, 1992
c22g2 Release July 7, 1992
c22g3 Release November 3, 1992
c22g4 Release March 1, 1993
c22g5 Release August 1, 1993
CHARMM23.0
c23a1 Developmental August 15, 1992
c23a2 Developmental October 25, 1992
c23f Developmental March 1, 1993
c23f1 Developmental March 15, 1993
c23f2 Developmental August 15, 1993
c23f3 Release February 1, 1994
c23f4 Release August 15, 1994
c23f5 Release March 15, 1995
CHARMM24.0
c24a1 Developmental February 15, 1994
c24x1 Evaluation February 15, 1994
c24a2 Developmental August 15, 1994
c24a3 Developmental March 15, 1995
c24b1 Release August 15, 1995
c24b2 Release February 15, 1996
c24g1 Release August 15, 1996
c24g2 Release February 15, 1997
CHARMM 25.0
c25a0 Developmental August 15, 1995
c25a1 Developmental February 15, 1996
c25a2 Developmental August 15, 1996
c25a3 Developmental February 15, 1997
c25b1 Release August 15, 1997
------------------------------------------------------
* Menu:
* C21-C22:: Modifications of Developmental CHARMM21 to CHARMM22
* C20-C22:: Major enhancements and developments in CHARMM22
* C22-C23:: Major enhancements and developments in CHARMM23
* C23-C24:: Major enhancements and developments in CHARMM24
* C24-C25:: Major enhancements and developments in CHARMM25
Summary of Modifications of Developmental CHARMM21 to CHARMM22
------------------------------------------------------------------------------
Linear pressure ramping added to CPT code (see pressure.doc)
------------------------------------------------------------------------------
Frequency based crystal update is now supported
Relevent new keyword is IXTFrq (see image.doc)
------------------------------------------------------------------------------
Constant Pressure and Temperature (CPT) dynamics (See PRESSURE.DOC)
TRICLINIC unit cell is now supported.
------------------------------------------------------------------------------
Miscellaneous commands:
UPPEr and LOWEr keywords added (see miscom.doc)
------------------------------------------------------------------------------
Minimization: new keyword (FMEM) for ABNER minimizer (see minimiz.doc)
------------------------------------------------------------------------------
Internal coordinates (see INTCOR.DOC)
New commands:
IC SAVE
IC RESTore
IC RANDom [iseed]
Internal coordinates converted to double precision.
------------------------------------------------------------------------------
Coordinate Manipulation (See MISCOM.DOC and CORMAN.DOC)
New inline command varaibles added:
?THETa , ?XMOVe , ?YMOVe , ?ZMOVe , ?RMS
New CORMAN commands added:
COOR HELIx
COOR PUCKer
COOR COVAraince
COOR SEARch ... RBUFF ...
------------------------------------------------------------------------------
Energy, Angles
Urey-Bradley 1-3 terms have been added as an option.
Format of parameter file affected. (See IO.DOC)
Energy analysis code added (ANALysis ON command). (See ANALYS.DOC)
------------------------------------------------------------------------------
NOE distance restraints (See CONS.DOC)
Overhaulled to become a general distance restraint term.
Commands syntax overhaulled as well.
------------------------------------------------------------------------------
PSF common structure modified
Unused PSF arrays removed. All size limits increased.
Binary file format changed to INTEGER*4 and REAL*8
PSF numbers added to ?variable list (See MISCOM.DOC).
------------------------------------------------------------------------------
Output redirecting implemented. (See MISCOM.DOC)
OUTU replaces all writes to unit 6.
------------------------------------------------------------------------------
ATLIM modified to allow a limit of several days.
PASMID has been changed to an integer which points the
current day. See MISCOM.DOC
------------------------------------------------------------------------------
Free energy perturbation commands added. (See PERT.DOC)
Several new commands and features have been modified
to allow free energy perturbation simulations to be performed.
------------------------------------------------------------------------------
Partition function and classical free energy codee added to the vibrational
analysis code. (See VIBRAN.DOC)
Atom selection added for EDIT commands.
Atom selection added for WRITE SECOnd-derivatives CARD command.
------------------------------------------------------------------------------
New time series commands and options (See CORREL.DOC)
ENTER PUCKer
ENTER HELIx
ENTER RMS
ENTER ENERgy
ENTER RMS [MASS] atom-selection
ENTER ATOM CROSsproduct
ENTER FLUC CROSsproduct
ENTER VECT CROSsproduct
ENTER HBOND
ENTER MODE
ENTER RMS [MASS] [ORIEnt]
...
TRAJ ... atom-selection
MANTIME SQUARE (vectors now allowed)
MANTIME ABS (vectors now allowed)
MANTIME ACOS
Off-by-one error removed in time series data (time series now do not start
at time zero, but at time DELTA*SKIP).
------------------------------------------------------------------------------
Langevin dynamics modified.
An improved algorithm has been incorporated which gives a more accurate
integration at low gamma values as well as the proper brownian dynamics
limiting values in the large gamma limit (and is more efficient).
The gaussian random generator has been replaced to give a much more
accurate distribution and uses only one random number call per atom
by using an error function lookup table.
------------------------------------------------------------------------------
Miscellaneous commands added. (See MISCOM.DOC)
DIVIde, EXONent, RANDom, and SHOW
New miscellaneous variables added.
?RAND,
------------------------------------------------------------------------------
Precision and index limits improved.
The entire program (except for the graphics section) has been
converted to REAL*8 and INTEGER*4 from REAL*4 and INTEGER*2.
------------------------------------------------------------------------------
Constant Pressure and Temperature (CPT) dynamics added. (See PRESSURE.DOC)
Pressure analysis code added.
NTRFRQ usage modified so that it works for IMAGES and CRYSTAL.
------------------------------------------------------------------------------
Heuristic nonbond update feature added. (See NBONDS.DOC)
------------------------------------------------------------------------------
New (consistent) energy print format with search line indicators.
------------------------------------------------------------------------------
Graphics subsection added for workstations.
------------------------------------------------------------------------------
New GRADient option added for most minimization methods for
searching for saddle points.
------------------------------------------------------------------------------
FAST option is now the default. It is no longer necessary to have the
command "FAST 1" in order to use the efficient energy routines.
------------------------------------------------------------------------------
Constrained reference now only set for selected atoms for the CONS HARMonic
command (the old method limited versatility). (See CONS.DOC)
------------------------------------------------------------------------------
Parallelization for shared memory multi-processor machines has been
implemented. Functionality for the fast energy routines has been increased.
The vector/parallel routines will now to no electrostatics and novdw
as well as simple cut-offs.
------------------------------------------------------------------------------
SPECIfy command. Controls various options such as I/O buffer flushing
maximum number of processors to be used and whether to use the fast
nonbond list generator.
------------------------------------------------------------------------------
SYSTem "unix bourne shell commands" This command permits the user to issue
Unix shell commands from the program. The command string must be enclosed
in double quotes to prevent the CHARMm parser from converting the string
to uppercase.
------------------------------------------------------------------------------
SHAKE FAST This command specifies the use of the new vector/parallel SHAKE
------------------------------------------------------------------------------
Deleted Features:
The old VAX analysis facility has been removed.
Sigma van der Waal switching and shifting options has been removed.
BARRI command removed.
------------------------------------------------------------------------------
Major Enhancements and Developments in CHARMM22
As CHARMM20 is not clearly defined, it is not straightforward to sort
out major differences between the current version of CHARMM
(CHARMM22.0) and a previous version (CHARMM20 or CHARMm21).
The VAX version CHARMM on HUCHE1 turns out to be a "developmental"
version towards CHARMM21 and contains the crystal facility, BLOCK, etc.
The following is prepared by comparing the developmental VAX version
CHARMM21 source code and that of CHARMM22.0.
Obsolete Modules Deleted from CHARMM20
--------------------------------------
[1] GRAMPS
It is supported only in the VAX version CHARMM20.
TH:[MK.PROT.SOURCE.VAX]GRAMPS.FLX contains an interactive routine that
writes several files for the command language interpreter for
producing computer graphics on the Evans & Sutherland
Multi-Picture-System called GRAMPS. This obsolete feature is no
longer supported in CHARMM22.
[2] PARAmeter Optimization
PARMOP is not incorporated in the VAX version CHARMM20 either except
at the point of command parsing. It seems that the feature has never
been included in the central version.
New Features in CHARMM22
------------------------
[1] BLOCK
The developmental CHARMM21 VAX version supports some BLOCK commands.
The BLOCK commands are used to partition the molecular system into
blocks and allows for the use of coefficients that scale the
interaction energies between the blocks. Specific commands to carry
out free energy simulations with a component analysis scheme have been
implemented.
[2] CRYStal
The CRYStal commands are used to build a crystal with any space group
symmetry, to optimize its lattice parameters and molecular coordinates
and to carry out a vibrational analysis. The CRYSTAL program is
incorporated into the IMAGE module. The VAX developmental version has
a separate CRYSTL module.
[3] COOR COVAri
The new COORdinate subcommand COVAriance is added. It computes
covariances of the spatial atom displacements of a dynamics trajectory
for selected pairs of atoms.
[4] CORR HELIx / CORR PUCKer
The New CORRelation commands HELIx and PUCKer are introduced. The
HELIx command computes time series of the helical axis orientation and
PUCKer computes that of the sugar pucker phase and amplitude.
[5] DRAW, GRAP
The new module GRAPHICS provides CHARMM the capability of displaying
molecular structures when run on a graphics workstation. (Currently
works only on Apollo machines.)
[6] HBTRim
The HBTRim command deletes hydrogen bonds that have an energy of
interaction that is higher than the specified cutoff. This command is
used to reduce a list of hydrogen bonds to that of important hydrogen
bonds.
[7] MOLVIB
MOLVIB is a general purpose vibrational analysis program, suitable for
small to medium sized molecules (less than 50 atoms). It performs
canonic force field calculations (KANO), crystal normal mode analysis
for k=0 (CRYS) and other vibrational analyses in internal coordinates
or in Cartesian coordinates. Details are documented in molvib.doc.
[8] PERT
The PERTurbe command allows the scaling between PSFs for use in energy
analysis, comparisons, slow growth free energy simulations, and
widowing free energy simulations. This is a rather flexible
implementation of free energy perturbation that allows connectivity to
change. Also, three energy restraint terms (harmonic, dihedral and
NOE) are subject to change which allows a flexible way in which to
compute free energy differences between different conformations.
[9] QUANTUM
Quantum mechanical and molecular mechanical combined force field
method is implemented by employing the semi-empirical SCF method of
the MOPAC program. This module has not been tested nor documented.
The code does not confirm CHARMM coding standards. The future of the
code is not certain at the time of the current release.
[10] RMSD
The new RMSDyn routine is a modified CORMAN routine by William D.
Laidig, which computes the RMS difference between two trajectory files
and make a matrix of results.
[11] RXNCOR
The RXNCor command is used for defining a reaction coordinate for any
molecule based on its structure and impose an umbrella potential along
that reaction coordinate (i.e., to run activated dynamics along this
coordinate) in order to trace out the free energy profile during the
structural change along the coordinate.
[12] SOLANA
The solvent analysis facility computes solvent averaged properties,
e.g., the solvent velocity autocorrelation function, mean-square
displacement function, solvent-solvent radial distribution functions,
solvent-reference site radial distribution function, and the solvent -
reference site deformable boundary force.
[13] TRAJ
The new TRAJectory command is used to merges or to break up a dynamics
coordinate or velocity trajectory into different numbers of units.
[14] TSM
The Thermodynamics Simulation Method module performs the free energy
simulation.
[15] Urey-Bradley Energy Term
Urey-Bradley 1-3 terms have been added. The developmental CHARMM21
also includes U-B terms.
[16] Update
Two new non-bonded neighbour list updating schemes are introduced; one
has something to do with an automated updating procedure and the other
with the list generation algorithm.
When INBFRQ is set to -1 (which is the default), heuristic testing
is performed every time ENERGY is called and a list update is done if
necessary.
A new routine NBNDGC (nbndgc.src), a modification of NBONDG, is
introduced. NBNDGC is based on a cubical grid searching algorithm and
generates the nonbonded list in linear time, as opposed to quadratic.
On the Convex C220, which is a vector machine, it is faster than
NBONDG for any system larger than a few hundred atoms.
[17] Integrator
The leap-frog integrator has been implemented. While the "old" Verlet
integrator is still available via the DYNA VERLet command (and is the
default), the new integrator can be accessed by DYNA LEAP. The velocity
Verlet integrator is also added in CHARMM. This new velocity Verlet
integrator can be called by DYNA VVER.
[18] Constant Pressure & Temperature Dynamics (DYNCPT)
The constant pressure/temperature dynamics algorithm is implemented
following the paper by Berendsen et al. (J. Chem. Phys. (1984) 81(8)
p.3684).
Modification of CHARMM20 to CHARMM22
------------------------------------
[1] ANALysis
The VAX version analysis facility is replaced by an energy
contribution array (ECONT). All evaluated energy terms are
partitioned into each atomic contribution and collected in the array,
which is accessible through the SCALAR command.
[2] XRAY
The XRAY command of CHARMM20 is replaced by the READ XRAY command in
CHARMM22. In CHARMM22, all I/O functions are parsed in mainio.src.
The subroutine XRAY is changed to RDXRAY, which generates a card file
compatible with Richard Feldmann's XRAY display program.
[3] NOE
NOE constraint has been overhauled. It now handles general distance
restraint terms.
[4] MISCOM
The miscellaneous command parser (miscom.src in CHARMM22) is modified.
(1) The SKIPE command is parsed in MISCOM.
(2) New command parameter (@x) handling commands are added: DIVIde,
EXPOnentiate, GET, MULTiply and SHOW.
(3) The RANDOM command is added to set random number specifications.
(4) The STOP command is parsed in MISCOM.
(5) The QUICk (or Q) command is added to carry out a quick coordinate
analysis.
[5] HANDLE
The subroutine HANDLE is improved to accept command line arguments
given with the CHARMM command issued to an operating system. It works
on most UNIX, UNICOS and VAX/VMS versions.
[6] Command Parameters
In CHARMM20, we have ten command parameters @n, where n is a single
digit, 0 through 9. It is expanded to support any single
alpha-numeric character so that one can use upto 36 command
parameters (0-9, a-z).
[7] Dynamic Memory Allocation
Most of UNIX versions now support VEHEAP. VEHEAP was originally
implemented by employing VAX/VMS system calls. It expands the HEAP
common block when more HEAP space is needed. In UNIX versions, we use
the UNIX system library routine malloc(), if available (the
availability depends on the machine), to perform the same function.
[8] File Format / Compatibility
All binary files except dynamics trajectory are written in double
precision format and not compatible with old versions. For PSF,
topology, parameter, etc. one should use CARD format to transfer
previous version files to CHARMM22. Trajectory files are written in
single precision and compatible with all CHARMM versions and QUANTA.
Old version dynamics restart files are not compatible with CHARMM22.
[9] Random Number Generator
All random number routines are implemented in double precision (64-bit
words). Box-Muller algorithm is used for generating a Gaussian random
deviat. A machine specific random number routine (RANV of CONVEX
VECLIB) is used in a CMU version.
Major Enhancements and Developments in CHARMM23
As an on-going project, CHARMM development has been carried out with
CHARMM version 23 series. CHARMM development entails two objectives.
First, we maintain an integrated macromolecular science package
running on a wide range of computing devices. Second, we incorporate
and exploit molecular simulation methodologies at the frontier of
current research.
In order to establish the first objective, we maintain all source
and support files under CVS (Concurrent Versions System) control. The
ROOT repository is tammy.harvard.edu:/prog/chmgr/CVS. CHARMM23 is
stored in /prog/chmgr/CVS/c23a. A particular version is retrieved
with the version name as the rivision tag (e.g., c23f3).
Since we branched out from the CHARMM22 release version c22g2, we
have made two alpha versions and four FORTRAN versions.
c23a1 Developmental August 15, 1992
c23a2 Developmental October 25, 1992
c23f Developmental March 1, 1993
c23f1 Developmental March 15, 1993
c23f2 Developmental August 15, 1993
c23f3 Release February 1, 1994
c23f3 is the current release version. As the "f" in c23f stands for
FORTRAN version, we converted FLECS source into FORTRAN. The
conversion task had been completed as of c23f2. Now CHARMM is written
in full FORTRAN except several machine dependant codes written in C.
The universal languages (C and FORTRAN) make it easier to port to new
machines in a broad range of architectural designs and to incorporate
new methodologies into a research version of CHARMM.
During the c23 development cycle, we have added and tested several
new features as described below. We have also ported c23 to new
machines and supported c23f versions on the following platforms.
Platforms Supported
-------------------
RREFX key Platforms
----------- -------------------------------------
ALLIANT Alliant
ALPHA DEC alpha workstation
APOLLO HP-Apollo, both AEGIS and UNIX
ARDENT Stardent
CONVEX Convex Computer
CRAY Cray Research Inc.
DEC DEC ULTRIX
HPUX Hewlett-Packard series 700
IBM IBM-3090 running AIX
IBMMVS IBM's MVS platform
IBMRS IBM RS/6000
IBMVM IBM's VM platform
IRIS Silicon Graphics
MACINTOSH Apple Macintosh computers (system 7)
SUN Sun Microsystems
VAX Digital Equipment Corp. VAX VMS
New Features in CHARMM23
------------------------
[1] Cray Fast Code
- Douglas J. Tobias
Vector/parallel code for energy calculation, shake, and nonbonded list
generation on the Cray was implemented. Dynamic heap and stack
allocation on the Cray was added.
[2] PARALLEL
- Bernard R. Brooks
General code for support of CHARMM on MIMD machines is completed.
This includes control of the I/O levels for all file I/O. For
parallel machines or workstation clusters, only node zero performs I/O
and it broadcasts are to other nodes.
All compuationally intensive code exercised in MD is now fully
parallel which includes: DYNAMC, ENERGY (and most subsections), SHAKE,
PRSSRE, DYNLNG, IMAGES,... Almost all comutationally intensive code
in the first order minimizers is fully parallel. Other usage of the
energy routines are parallel (such as the energy time series in CORREL).
[3] Dynamics Integrator
3.1 Leap-Frog Integrator
- Bernard R. Brooks
Berendsen's method was modified so that it would work for very
small systems and for very weak coupling constants. Now it is
possible to use SHAKE with CPT and get correct pressures and
temperatures. Another change is to calculate the change in potential
energy due to the constant pressure algorithm. The energy lost due to
the changes in box size is now added to the kinetic energy during the
constant temperature procedure. This allows the constant presure
code to nearly conserve energy and allows the constant temperature
code to be used with weak coupling times. This correction was made
when we found that water box simulations with the Berendsen's method
were running about 10 degrees too cold when both temperature and
pressure coupling times of 1ps were used. Now the correct target
temperature is achieved, even in the limit of very weak couplings.
3.2 EULER Dynamics Integrator
- Bernard R. Brooks
The incorporation of of the Langevin/Implicit Euler dynamics
integrator has been achieved. The effect is to remove the energy in
the high frequency degrees of freedom which eliminates the noise in
free energy studies where bonds are being modified. To support the
Implicit Euler integration, a Truncated Newton Minimizer has been
added. This minimizer may be used directly using the MINI TN command.
The minimizer is not yet fully implemented (it works, but is not as
efficient as it will be), but it is already very competitive relative
to existing minimization methods. MINI TN does not work with SHAKE.
This code has been developed by Tamar Schlick at NYU. It has been
integrated within CHARMM with some modifications.
3.3 EHFC: High Freequency Correction
- Bernard R. Brooks
The leap-frog dynamics integrator has been modified to have an
improved high frequency correction (HFC) term. With the old term,
energy was conserved within a harmonic degree of freedom, but total
energy would drift as energy exchanged between high and low frequency
degrees of freedom. The new code avoids this problem. The total
energy and kinetic energy that is printed in the first line of
dynamics energy printout has reverted to the standard Verlet energies,
and these match the output of the old integrator. The HFC terms
(total energy, and kinetic energy) are now printed on the second line.
The fluctuation of the HFC total energy is usually an order of
magnitude smaller than that of the total energy. The HCF total energy
is a good indicator of problems with NVE dynamics because small
changes in total energy are not lost in the noise of high frequency
oscillations.
3.4 Velocity Verlet Integrator
- Masa Watanabe
Velocity Verlet method has been implemented. Two integrator
(Verlet and Leap-frog) methods presented in CHARMM have their own
flavors, but Verlet method handles velocities rather awkward and may
introduce some numerical imprecision. On the other hand, the
Leap-frog integrator minimizes loss of precision on a computer, but it
does not handle the velocities in a satisfactory manner. Velocity
Verlet integrator can store positions, velocities, and accelerations
all at the same time and minimizes round-off error.
3.5 Nose-Hoover Constant Temperature Method
- Masa Watanabe
The constant temperature method has been implemented based on
S. Nose, JCP 81, 511 (1984) and W.G. Hoover, Phy. Rev. A 31, 1695 (1985).
This is an another type of constant temperature method, but an
equilibration time in the vicinity of the desired temperature is
faster than other routines which are available in CHARMM. Also
multi-temperature controls are also developed in order to equilibrate
the system faster and keep the system in the desired temperature well.
This method works with Verlet and Velocity Verlet integrators.
3.6 Multiple Time-Scaled Method
- Masa Watanabe
Tuckerman et al proposed a reversible RESPA algorithm recently
(Tuckerman, Berne, Martyna, JCP 97, 1990 (1992)). Previous MTS
methods have the disadvantages of loosing accuracy due to the
approximation of holding the slow variables fixed while integrating
the equations for the fast variables. But in this reversible RESPA
equations of motions are derived from Liouville operators and Trotter
theorem. The method gives more accurate dynamics than previous
methods. In this implementation, one can specify up to three
different time steps in dynamic simulation run.
[4] RISM (Reference Interaction Site Model)
- Georgios Archontis
The RISM module allows the user to calculate the site-site radial
distribution functions g(r) and pair correlation functions c(r) for a
multi-component molecular liquid. These functions can then be used to
determine quantities such as the potential of mean force or the cavity
interaction term between two solute molecules into a solvent, and the
excess chemical potential of solvation of a solute into a solvent. The
change in the solvent g(r) upon solvation can be determined and this
allows for the decomposition of the excess chemical potential into the
energy and entropy of solvation.
[5] MMFP (Miscellaneous Mean Field Potential)
- Benoit Roux
The MMFP Commands are primarily used for setting up special
restraining potentials on some or all of the atoms. The key word MMFP
is used to enter the MMFP environement. In the MMFP environment, all
miscelaneous commands (label, goto, if, etc...), and string
substitutions (with @1, @2, etc...) are supported. The key word END
returns to the main parser. The restraining potentials are used in all
energy calculations, unless SKIP is used. The subcommand RESET clears
the potential. This module is still under developement and only the
subcommand GEO is released. The subcommand GEO (standing for
geometrical) is used to setup various restraining potential
(spherical, planar or cyclindrical restraints) on some or all atoms.
The selection specification should be at the end of the command. The
default atom selection includes all atoms. Future subcommands will
include continuum electrostatic reaction field and solvent mean field
potentials. Expected date of release is Spring 1994.
[6] NMR Analysis
- Benoit Roux
The NMR commands may be used to obtain a set of time series for a
number of NMR properties from a trajectory. Among the possible
properties are relaxation rates due to dipole-dipole fluctuations (T1,
T2, NOE, ROE), chemical shift anisotropy and Deuterium order
parameters for oriented samples.
[7] REPLICA
- Leo Caves
Tool to support LES and MCSS calculations. Performs replication
of arbitrary regions of PSF. Data structure interfaces to non-bond
list generation routines, to perform appropriate exclusions. In
association with BLOCK can provide appropriate energy/force
normalizations for various classes of methods employing replicas.
Introduced REPLICA and REPDEB preprocessor directives. Code for
cray multi-tasking list generation routine used inference and has not
been tested. Convex parallel code works fine. Added miscellaneous
parameters to report number of atom/group pairs from non-bonded
routines: ?NNBA, ?NNBG, ?NNBI for atom/group/images respectively. For
replica-based exclusions from the list there are ?NRXA and ?NRXG for
atom and group exclusions.
[8] Clustr code integrated into CORREL
- Charles L. Brooks III
The CLUSTER command clusters time series data obtained within the
CORREL facility. The data are grouped into sets with similar time
series values, using euclidean distance as the dissimilarity measure
between different time frames of a set of time series. It is useful,
for example, for grouping together similar conformations or energy
levels.
[9] GRAPHICS
- Richard M. Venable
Graphics code converted to FORTRAN and overhauled. Versions that
work with Xwindows and GL are in progress. A new preflx keyword,
NODISPLAY, builds a version which produces HPGL, PLUTO FDAT, and
LIGHT.atm files without requiring any screen display capabilities.
The SG (IRIS) code incorporation is relatively untested. Postscript
file output similar to HPGL (but much nicer looking, hopefully) is
also implemented.
Major Modifications
-------------------
[1] Command Line Handling
1.1 Extension of Command Line Parameter Handling
- Leo Caves
A command line parameter token can now be a string rather than
just one of the single characters 0-9 and A(a)-Z(z). For substitution,
a token is indicated by the use of the @ character as before. The
token is end-delimited by any non-alphanumeric character. In the case
that the token is not found in the parameter table, a check is made to
see if the first character of the token is itself a token in the
parameter table. If this single character token is in the table, the
corresponding value is substituted -- this is the necessary scheme to
allow backwards compatibilty with the old parameter substitution,
which allowed parameters embedded in strings. For unambiguous token
detection, "protect" the token with brackets {} --- this allows for
the use of non alphanumerics in tokens such as -, _.
1.2 New Parsing Options
- Bernard R. Brooks
The IF command will be expanded to allow commands such as:
IF ?ENER .GT. ?VDW THEN GOTO label
or
IF ?NSEL .LT. 8 THEN GOTO label
1.3 MSCNUM
- Bernard R. Brooks
New code for flexible miscellaneous command substitutions has been
fully incoporated. Additional types were needed to make this code more
flexible. Three types are supported, REAL(*8), INTEGER, CHARACTER.
There are three subroutines which can be called; integer (SETMSI),
character (SETMSC), and real (SETMSR) to specify a command substitution
variable. Now it is possible for ?NATOM to return an integer, ?RSM to
return a real number, and ?SEGID to return the segment identifier of the
first selected atom.
[2] QUANTUM
Quantum mechanical and molecular mechanical combined force field
method was implemented by employing the semi-empirical SCF method of
the MOPAC program in the CHARMM version 22. The QUANTUM code has been
modified extensively to meet CHARMM standards.
There were several problems with the quantum code that have been
fixed. The van der Waal group nonbond list was missing due to an
improper interpretation of the group-group exclusion list in CHARMM
(It's a two state list, not a 3 state as in the atom-atom exclusion
list). All vdw interactions between QM and MM group where any QM atom
had an exclusion or a 1-4 interaction with any MM atom were not
computed. This caused major problems in certain situations where
there was a strong electrostatic attraction with no compensating vdw
interaction.
New code to add link and place link atoms has been written.
[3] Frequency Based Crystal Update
- Ryszard Czerminski
The modification allowes for automated, frequency based, crystal
update. New variable (IXTFRQ) is introduced which controls frequency
of the crystal update.
[4] Ability to Linearly Increase/Decrease Pressure
- Ryszard Czerminski
The goal was to allow for linear increase (decrease) of the
pressure during single dynamic run. New variables/keywords were
introduced (PIXX - initial value of XX component of pressure tensor,
PFXX - final value etc... for other components).
[5] Atom Selection
5.1 Atom Parse
- Bernard R. Brooks
A new atom name parsing subroutine has been developed. This makes
the code simpler and facilitates further advancements in atom
parsing. One new feature allows an atom selection to be used to
select a series of atoms. This is very useful in CORREL for
specifying clusters of atoms for analysis. When the atom selection
feature is used to specify 4 atoms of a dihedral, the first 4 selected
atoms will be chosen.
5.2 New Tokens
- Bernard R. Brooks
new operator; .BYGROUP. <factor>
new token; IGROup <int1> : <int2>
have been added to allow the selection of atoms based on electrostatic
groupings.
Several keynames have been added to allow the query of the
characterstics of selected atoms;
?SELATOM - number of first atom selected
?SELIRES - number of first residue selected
?SELISEG - number of first segment selected
?SELTYPE - name of first atom selected
?SELRESI - resid of first residue selected
?SELSEGI - segid of first residue selected
?SELRESN - residue type of first atom selected
?SELCHEM - chemical type of first atom selected
These new keywords are in addition to the existing keyword;
?NSEL - Number of atoms selected
[6] Correlation
6.1 New MANTim Options in CORREL
- Bernard R. Brooks
A histogram option to time series manipulation has been developed.
This is executed by the command;
MANTime time-series-name HISTogram min-value max-value num-steps
The selected time series is replaced with a histogram which contains
the probability of finding the time series within a given value range.
Also, new options (RATIo and KMULt) added to the CORREL MANTIME command.
6.2 Dihedral Time Series in CORREL.
- Bernard R. Brooks
Fixed problems with the diheral code in correl to account for
torsional timeseries. The correct fluctuation is now determined.
The extra processing has been removed from the SHOW command because
the data may no longer be valid for this processing when MANTIME
commands are present in a script. A new command option "MANTime
CONTinuous-dihedral" has been added to allow a dihedral timeseries to
be unfolded to a continuous function.
6.3 Extension of Solanal ANALysis command
- Arnaud Blondel
A command -CROSs- was added to allow a cross analysis on two
selected subsets of atoms. For the moment the exclusion of the couple
of atoms belonging to the same SEGId is not implemented. The keyword
CROSs cannot be selected with the following options: WATer, SITE,
IKIRkg, ISDIst, IFDBf. IVAC, IMSD and IFMIn have not been tested with
CROSs.
[7] SCALAR Command Enhancement
- Bernard R. Brooks
The ASP arrays (IGNOre, ASPV and VDWS) are now accessible. There
is a sort option for the SHOW command. There is a new MASS keyword
for the STATistics and AVERage commands
A new SCALAR READ option has been added. It allows values to be
entered from a file. The use is:
OPEN READ CARD UNIT 12 NAME file.dat
SCALar WMAIn READ 12 SELE ... END
which will read selected entries to the weighting array.
[8] SURFACE
- Bernard R. Brooks
New analytic surface area code and energy terms for ASP (Atomic
Solvation Parameters) energy and forces have been fully integrated
(and parallelized for multi-machines). This has been achieved by the
incorporation and adaptation of the code from Wesson and Eisenberg.
The default for the COOR SURFace command is now the analytic surface
area. The anaylitic answer is less expensive and more accurate. The
older Lee and Richard's algorithm may still be invoked by specifying a
nonzero RPRObe value. The maximum number of contacts that a sphere
may have has been increased from 15 to 35.
[9] QAUGMENT
- Bernard R. Brooks
It is desirable for a patch to be able to augment the charge of an
atom. The current code could only set a charge. The new code can add
or subtract a value from the charge. This is done by using a patch
charge value near 100.0. For example, a charge of 100.15 will add
0.15 to the current charge. A charge value of -101.0 will subtract 1.0
from the current charge. Charge values less than -90.0 or larger than
90.0 are no longer allowed for generate or patch without charge
augment. It allows more flexible patches to be developed where the
prior charge on modified atoms need not be known.
[10] COORdinate Commands
10.1 VACUUM_OP: COOR SEARCH Subcommand
- Bernard R. Brooks
The ability to manipulate pixel bitmaps generated from the COOR SEARCH
command has been developed. The new syntax for the COOR SEARCH command is;
COOR SEARch {PRINt [UNIT int]} { } {[VACUum]} {[RESEt]} [SAVE]
{[NOPRint] } {[RCUT real]} { FILLed } { AND }
{[RBUFf real]} { HOLES } { OR }
{ XOR }
The new keywords are;
SAVE - save the resultant bitmap for subsequent operations
AND - logical AND the new bitmap with the previously saved map
OR - logical OR the new bitmap with the previously saved map
XOR - logical XOR the new bitmap with the previously saved map
HOLES - search for holes (vacuum points surrounded by filled points)
10.2 New COOR DIST command
- Bernard R. Brooks
The COOR DISTance command has been overhauled and has additional
features. One such feature is the ability to get g(r) plots from
trajectory files using atom selections. It has several other
features. The new syntax is:
COOR DISTance
{ WEIGhting vector-spec atom-selection }
{ }
{ [UNIT int] [CUT real] [ENERGy [CLOSe]] 2X(atom-selection) - }
{ [Nonbonds] } { [NO14exclusions] } { [NOEXclusions] } -
{ NONOnbonds } { 14EXclusions } { EXCLusions }
[TRIAngle] [ HISTogram HMIN real HMAX real HNUM integer -
[HSAVe] [HPRInt] [HNORm real] [HDENsity real] ]
[11] JOIN/RENUMBER Command
- Bernard R. Brooks
A "JOIN segid RENUMBER" feature is added in the JOIN command.
This allows resid's to be made sequential within a single segment.
[12] PREFX.SRC overhauled.
- Bernard R. Brooks
The PREFX program has been overhauled. The new code has the
following features:
- It allows "!" comments at the end of valid FORTRAN statements.
- Conversion to single precision is performed ONLY if the SINGLE
keyword is present.
- It allows the use of identifier comments in ## statements.
For example:
##IF PERT (pertprint)
...
##ELSE (pertprint)
...
##ENDIF (pertprint)
This makes the code easier to read and allows ##ENDIF statements to be
uniquely identified. A fatal error is flagged if the identifiers do
not match.
Major Enhancements and Developments in CHARMM24
During the C24 development cycle, February 15, 1994 to February 15, 1996,
we made two bugfix-updates in the c23 releases and three alpha versions
and one beta version in the c24 development line. c24x1 is the MMFF
implementation in CHARMM developed at the Molecular Simulations Inc.
CHARMM23.0
c23f4 Release August 15, 1994
c23f5 Release March 15, 1995
CHARMM24.0
c24a1 Developmental February 15, 1994
c24x1 Evaluation February 15, 1994
c24a2 Developmental August 15, 1994
c24a3 Developmental March 15, 1995
c24b1 Release August 15, 1995
Only bugfixes are incorporated into CHARMM23 and all new developments
and enhancements have been carried out with the CHARMM24 developmental
versions. All modifications are thoroughly recorded in the
ChangeLog.c24 file and the following is the summary of new features
and major enhancements in CHARMM 24.
New Features in CHARMM24
------------------------
[1] New Ports and Parallel Versions
1.1 Enhancement to Parallel Code
- Bernard R. Brooks and Milan Hodoscek
There has been continued development of the parallel code for
CHARMM. This includes new features run in parallel, new machine types
supported, new parallelization methods, and code made to run more
efficiently. Due to conflict in routine names with library routines,
the subroutines: WRITEC and READC had to be renamed.
Initial code to allow the use of the Terra parallel computer has
been added. Added preflx keyword SGIMP for multiprocessor SG machines
using PVM massage passing library. The difference between PVM and
(SGIMP, PVM) is that all the processes are spawned on one host and
some communication parameters are not supported on MP machines. It can
be used on a single processor SG for testing purpose. Use PVM only on
a cluster of any type of workstation.
1.2 Convex Exemplar SPP-100 and generic PVM Ports
- Charles L. Brooks, III and Stephen H. Fleischman
A port of CHARMM version 24a2 to general PVM based parallelism
using existing parallel code as well as a port to the Convex parallel
machine are included.
1.3 Cray T3D Port
- Charles L. Brooks, III and Barry C. Bolding
A port of CHARMM version 24a2 to the Cray T3D parallel computer using
existing parallel code is included.
1.4 Port of parallel CHARMM to Convex Exemplar SPP-1000 and generic MPI
- Charles L. Brooks, III and Stephen H. Fleischman
A port of CHARMM version 24a3 to general MPI based parallelism
using existing parallel code as well as a port to the Convex parallel
machine are included.
1.5 Thinking Machine's CM5 Port
- Robert Nagle
Previous communication scheme was based on a simple send and
receive model. By using TMC's active message layer, communication
bandwith can be increased by anywhere from 50% to 5X.
1.6 OS/2 Port
- Stefan Boresch
CHARMM (c23f4 and c24a3) has been ported to the OS/2 operating
system, version 2.x and higher. The Watcom Fortran compiler (v. 9.5,
patch-level (c)) has been used. A new pre-processor keyword, OS2, has
been introduced, and all OS/2 related changes hide behind the OS2
keyword. There is currently no install script. Please contact me
if you want to build an OS/2 version of CHARMM (boresch@tammy.harvard.edu).
[2] Fast Multipole Code for Electrostatic interactions
- Robert Nagle
This is an initial implementation of a fast multipole method,
based on John Board's work. A new non-bond option (FMA) has been added.
This replaces cut-off parameters with a no cut-off hierarchical
technique. The advantages of this method are that you can control the
error and that it is amenable to parallelization. FMA is an O(N)
technique but the constant is large and so FMA will, in general, be
slower for systems of less that 5000 atoms, for the same accuracy.
Two options, LEVEL and TERMS, govern how many hierarchical levels
are used and how many terms are retained in the expansion, respectively.
In the method, each box at every level is subdivided into 8 sub-boxes
- you should select LEVEL so that the boxes at the lowest (i.e.
finest) level contain 10-20 atoms on average: 3 or 4 will be typical
choices. You then select TERMS to control the accuracy that you
require: 4 will often suffice but I would generally recommend 6 or
even 8. See the references in fma.doc for a detailed description of
the error bounds.
NOFMA is the nonbond option which turns off the multipole method.
Compilation of FMA is controlled by the flag, FMA, in pref.dat.
FAST ON is required for this initial implementation. This
implementation is not yet parallelized.
[3] Energy Embedding by the Addition of a Higher Spatial Dimension
- Elan Z. Eisenmesser / Carol Post
The energy embedding technique entails placing a molecule into a
higher spatial dimension [Crippen, G. M. & Havel, T. F. (1990) J.
Chem. Inf. Comput. Sci. Vol 30, 222-227]. The possibility of
surmounting energy barriers with these added degrees of freedom may
lead to lower energy minima.
With the recent success of using four dimensions in the GROMOS
force field [Van Schaik, R. C., Berendsen, H. J. C., Torda, A. E., &
van Gunsteren, W. F. (1993) J. Mol. Biol. Vol 234, 751-762], creating
a similar option in CHARMM should also prove advantageous.
Specifically, another cartesian coordinate was added to the usual X,
Y, and Z coordinates and was appropriately named FDIM for Fourth
DIMension. This implementation has led to alterations in some
existing code along with the addition of several algorithms.
[4] DIMB (Diagonalization In a Mixed Basis) Method
- David Perahia, Liliane Mouawad, Herman van Vlijmen
The DIMB (Diagonalization In a Mixed Basis) method (see L. Mouawad
and D. Perahia (1993), Biopolymers, 33, 599) is an iterative method to
calculate the N lowest normal modes of molecules. It is especially
targeted to do large molecules, since it does not require the full
Hessian to be stored in memory or on disk. In short, the method
does repetitive reduced-basis diagonalizations in bases that consist
partially of the approximate eigenvectors, and partially of Cartesian
coordinates. Eigenvectors are saved to file during the process. Before
that is done, a new basis is again created, which consists of the
approximate eigenvectors at that point + the residual vectors (Lanczos
vectors). This accelerates the convergence. A very good property of
this method is that the final eigenvectors are as accurate as the user
wants them to be, so the results are no different from a full-blown
diagonalization.
Because the method is iterative, it takes longer to converge than
a regular diagonalization. Sizewise it can handle almost anything on
a moderately sized computer. David Perahia calculated a few dozen modes
of Hemoglobin (~600 residues = ~6000 atoms = ~18000 d.o.f.) on a
SGI workstation with 90 Mb memory. I have done several calculations
on 900 residue systems. The actual time to reach convergence depends
on the available memory, the desired accuracy, and the number of
requested normal modes.
One other area where the method saves memory is in the storage of the
original Hessian. Since this matrix is usually sparse for large systems,
a compressed Hessian is set up, which contains all non-zero elements.
In addition, I added the option to used this compressed Hessian in the
reduced-basis diagonalization option of VIBRAN. Before, the same size
limits applied to full diagonalizations and reduced-basis diagonalizations.
This should not be: people usually want to do reduced-basis calculations
because the molecule is too big for the Hessian to be stored in memory.
The option VIBRAn REDUce CMPAct will fill the compact Hessian and
form the reduced-basis Hessian from this compact Hessian. Overall, this
is a big saving on memory space.
[5] Arithmetic Expression Interpreter
- Benoit Roux
An interpretor of arithmetic expression has been added to the
CHARMM command parser. It is called at the level of the miscellaneous
command handling using simply by the word CALC (for calculator).
It can be used to evaluate algebraic numerical expression. The command
supports all mathematical numerical expression with arbitrary number
of nesting of recursive parentheses, e.g.,
exp[1.0-cos(2*(log(2*pi))**2)/0.5]
The parsing is actually very crude since the expression is translated
back and forth between character string and a real variable to handle
the logic (there is no real subroutine recursion).
[6] TNPACK Update
- Tamar Schlick, Phillipe Derreumaux and Eric Barth
The truncated-Newton minimization package TNPACK, developed by
T. Schlick and A. Fogelson, has been incorporated into CHARMM and
adopted for biomolecular energy minimization. TNPACK is based on the
preconditioned linear conjugate-gradient technique for solving the
Newton equations. The structure of the problem --- sparsity of the
Hessian --- is exploited for preconditioning.
Thorough experience with the new version of TNPACK in CHARMM has
been described in a paper now in press in the Journal of Computational
Chemistry: Applications are reported for a series of molecular systems
including Alanine Dipeptide (N-Methyl-Alanyl-Acetamide), a dimer of
N-Methyl-Acetamide, Deca-Alanine, Mellitin (26 residues), Avian
Pancreatic Polypeptide (36 residues), Rubredoxin (52 residues), Bovine
Pancreatic Trypsin Inhibitor (58 residues), a dimer of Insulin (99
residues), and Lysozyme (130 residues). Through comparisons among the
minimization algorithms available in CHARMM, we find that TNPACK
performs significantly better than ABNR in terms of CPU time when
curvature information is calculated by a finite-difference of
gradients (the "numeric" option of TNPACK). The CPU gain is 50% or
more (speedup factors of 1.5 to 2.5) for the largest molecular systems
tested and even greater for smaller systems (CPU factors of 1 to 4 for
small systems and 1 to 5 for medium systems). With the analytic
option, TNPACK converges more rapidly than ABNR for small and medium
systems (up to 400 atoms) as well as large molecules that have
reasonably good starting conformations; for large systems that are
poorly relaxed (i.e., the initial Brookhaven Protein Data Bank
structures are poor approximations to the minimum), TNPACK performs
similarly to ABNR.
TNPACK uses curvature information to escape from undesired
configurational regions and to ensure the identification of true local
minima. It converges rapidly once a convex region is reached and
achieves very low final gradient norms, such as of order 10E-8, with
little additional work. Even greater overall CPU gains are expected
for large-scale minimization problems by making the architectures of
CHARMM and TNPACK more compatible with respect to the
second-derivative calculations.
This work should be the focus of future developments. Such work
involves sparse storage of the Hessian, efficient sparse
Hessian/vector multiplications, and separation of the gradient and
Hessian calculations.
[7] X-window graphics extensively modified.
- Richard M. Venable
Several new features have been added to the X-window version of CHARMM
graphics. This code has also been tested on a wider variety of
hardware platforms (for example: SGI).
Changes include: double-buffering, clipping, StaticColor, symbol fonts,
window title, modified colormap calls, and a misc. Bug fixes in the
labeling of the X axis. A NODISPLAY compile option has been added to
the X windows version of CHARMM graphics in which only derivative
files are produced. The GRAPhics NOWIndow option can be used to
generate the same effect at run time.
[8] Minimum Image Periodic Boundary Code
- Charles L. Brooks, III, William A. Shirley and Stephen H. Fleischman
Simple minimum periodic boundary conditions are added for cubic,
truncated octahedra and rhomboidal (dodecahedra) periodicities which
augments the image facility and enhances parallel scaling on scalar
parallel machines as well as significantly reducing the memory
requirements. This code is developed and fully tested for the
simulation cells described above when the cell edgelength is the same
in all dimensions. The (trivial) extension to non-identical cell
sides will be added. However, it is critical to see reasonable
performance on all scalar parallel platforms where simulations using
images are currently employed that this enhancement be added now.
[9] GAMESS Code
- Bernard R. Brooks and Milan Hodoscek
The CHARMM-GAMMES interface is under development. The interface
part is completed and testing is in progress.
Major Enhancements in CHARMM24
------------------------------
[1] New Dihedral / Improper Dihedral Energy Routines
- Arnaud Blondel
The previous energy routines used the derivatives d(cos(phi))/dr
to calculate the forces and the second derivatives. This choice
introduced an artificial singularity at sin(phi)=0.
The new routines use the derivative d(phi)/dr and thus have no
singularities. This removes the tests to avoid numerical overflow or
the switch functions in the vector improper routines.
The new dihedral routines now support cases where planar conformation
is not an extremum. Thus a value other than 0 or 180 can be specified
in the dihedral parameters. The dihedral constraints can also use the
dihedral functional form using the key word PERIod and giving a
non-zero number.
[2] Extended Pressure System, Langevin Piston Code
- Bernard R. Brooks, Scott E. Feller and Yuhong Zhang
The constant pressure code has been overhauled. The old method
based on Berendsen's method has been replaced with a Langevin Piston
Method. When no friction is applied, this method becomes the standard
method based on Nose and Klein (adapted from Andersen). At the limit
of infinite friction with no random force, this reverts to the
Berendsen method.
The unit cell information has been added to the trajectory file
format. This implementation required an update to the image and
crystal code which cleaned up some ancient problems. Options for
including the surface tension (gamma-Area) term is also completed and
tested. This has been developed for the accurate simulation of
interfacial systems.
[3] Anisotropic Harmonic Restraints
- Bernard R. Brooks
The global scale factors: "XSCAle", "YSCAle", and "ZSCAle" have
been added to the "CONS HARM" command. This allows using the CONS
HARM to enforce a planar or linear restraint. This feature is also
useful for use in conjunction with our COORPLAS program (for generating
3-D coordinates from plastic models).
[4] New RESDistance Facility
- Bernard R. Brooks
A new facility, RESD, has been created to allow general distance
restraints based on a linear combination of distances. This is useful
for searching reaction pathways.
[5] New READ PARAm APPEnd Option
- Bernard R. Brooks
An append option has been added to the READ PARAM CARD command.
This allows just a few parameters to be modified without editing an
entire parameter file. A modification to the binary parameter file
format was necessary. Old binary files may not be appended, but they
are still supported.
[6] New READ PSF APPEnd Option
- Bernard R. Brooks
An append option has been added to the READ PSF command. This allows PSFs
to be easily merged to make a larger PSF. No modification to the binary
parameter file format was necessary. This option works with both FILE
and CARD options.
[7] Best Fit Option to CORREL TRAJectory Command
- Bernard R. Brooks
The TRAJectory command in correl now accepts an ORIENt keyword with an
optional [MASS] qualifier in conjunction with a second atom selection
that will best fit selected atoms with respect to the rms deviation
from the reference structure (in the comparison coordinate set). This
operation is done prior to the determination of any time series value.
This operation will not affect any time series value that is based
only on relative distances and angles.
[8] QM/MM Exclude Group Option
- Bernard R. Brooks
An option EXGRoup has been added which causes all atoms in the group
of the link atom host to be excluded from the QM/MM electrostatic
interaction terms. Code for specifying the charge of link atoms and
their placement has also been added.
[9] Enhancements to the Ewald Code
- Bernard R. Brooks, Scott E. Feller and Steve Bogusz
The EWALD electrostatic option now runs efficiently for parallel
architectures. Also, the maximum K-space values can be specified
independently for each direction. Several bugs were fixed.
Additional ways to compute ERFC() were added, including a lookup
table.
[10] MMFP/SSBP Upgrade
- Benoit Roux and Dmitrii Beglov
The Miscellaneous Mean-Field Potentials (MMFP) has been upgraded.
The spherical solvent boundary potential (SSBP) has also been
incorporated into EPERT. A new "membrane-like" planar potential
has been introduced using Gaussians to provide a smooth free energy
function based on hydropathy profile of individual amino acids
and solvent exposure. This is useful to orient membrane proteins.
A new primary shell of hydration has been added to the MMFP facility
to provide one layer of solvent around a flexible polypeptide.
For more information, see Beglov & Roux, Biopolymers 35: 171-178 (1995).
A solvent boundary potential for the simulation of water at
constant pressure is also added to the Miscellaneous Mean Field
Potential module. The boundary potential is an approximation but
follows from a rigorous statistical mechanical treatment of the
boundary. In light of the difficulties raised by the previous
treatments, a different route was chosen to formulate and develop the
solvent boundary potential for computer simulations of a finite
representation of an infinite bulk system. The present theoretical
formulation is based on a separation of the multidimensional
solute-solvent configurational integral in terms of n "inner" solvent
molecules nearest to an arbitrary solute, and the remaining "outer"
bulk solvent molecules.
This formulation, which differs significantly from previous
treatments, provides further insight into the statistical mechanical
basis of the solvent boundary potential and is helpful in constructing
useful approximations for computer simulations in dense liquids.
An approximation to the solvent boundary potential is constructed for
simulations of bulk water at constant pressure, including the
influence of van der Waals (done with RISM) and electrostatic
interactions (done with a Kirkwood-like multipole expansion).
The approach has been tested with success on several typical systems
(water, ions, n-butane and alanine dipeptide).
[11] Upgrade of the NMR module
- Benoit Roux
The NMR module is upgraded to have better output style. The old
version used the value of PRNLEV to choose the printed quantities.
Since this was a non-standard style in CHARMM, a series of logical
flags have been included in the command calls to print some chosen
quantities. In addition, the chemical shift anisotropy (CSA, used in
solid state NMR of membrane proteins in oriented samples) has been
redefined in term of a zmatrix to prevent confusion. The deuterium
quadrupolar splittings (DQS) command is also upgraded. A bug in a
call to NORMAL was fixed.
[12] New Options to CORREL
- Lennart Nilsson
Two new MANTime options have been added to CORREL: CROS and DOTP.
CROSsprod name Q(T) = Q(T) x Q2(T) produces the 3D crossproduct of
the two 3D vectors formed by the selected and named timeseries and
DOTProd name Q(T) = x-comp of Q(T)= Q(T) . Q2(T) gives x-comp of Q2(T)
angle in degrees between the two vectors.
[13] The COOR HBONd Command
- Lennart Nilsson
An option for the analysis of H-bond patterns from trajectories
has been added to corman.
COORdinates HBONd 2X(atom-selection) [CUT <real>] [CUTA <real>]
[IUNIt <int>] [BRIDge <resnam>]
[FIRSt int] [NUNIts int] [NSKIp int] [BEGIn int] [STOP int]
The HBONd command analyses a trajectory for hydrogen bonding
patterns. For each acceptor/donor in the first selection the average
number and average lifetime of hydrogen bonds to any atom in the
second selection is calculated. A hydrogen bond is assumed to exist
when two candidate atoms are closer than the value specified by CUT
(default 2.4A, (reasonable criterion, DeLoof et al. (1992) JACS 114,
4028), and if a value for CUTAngle is given the angle formed by D-H..A
is greater than this CUTAngle (in degrees, 180 is a linear H-bond);
the default is to allow all angles. The current implementation
assumes that hbonding hydrogens are present in the PSF and also uses
ACCEptor and DONOr information from the PSF to determine what pairs
are possible.
If output is wanted to a separate file the IUNIt option can be
used. If the BRIDge option is used the routine calculates average
number and lifetime of bridges formed between all pairs of atoms in
the two selections; a bridge is counted a residue of the type
specified with the BRIDge <resnam> hydrogen bonds (using same
criteria as for direct hbonding) to at least one atom in each
selection. The typical use of this would be to find water bridges.
Here again, results are presented for each atom in the first selection.
In order not to find hbonds between bonded atoms UPDATE is
called, which requires coordinates to be present when invoking this
module. Since this is done just to get the non-bond exclusion lists,
the cut-offs are set to very small values, and could influence
subsequent energy evaluations if the non-bond cutoffs are not then
respecified.
[14] NORESET Option for SHAKE
- Lennart Nilsson
The NORESET option is added to allow multiple shake commands.
It is useful to be able to define shake on bonds, bonh or so on
several different sets of atoms, with different shake options. The
NORESET keyword to shake command allows this by not zeroing counter.
[15] Trajectory Reading
- Lennart Nilsson
READCV is modified to read coordinates at multiples of skip FROM
the actual first coordinate set in a trajectory file.
[16] Make BLOCK work with IMAGE/CRYSTAL and vice versa
- Stefan Boresch
In order to make BLOCK work / coexist with the IMAGE module two
things had to be changed: (1) A memory allocation problem in the BLOCK
datastructure and (2) the post-processing modules needed to be
overhauled to allow for nonbonded list updates while reading frames
from the trajectory.
Ad (1), memory allocation: BLOCK uses two data-structures, one
containing the interaction matrix between blocks, and one containing
the block number for each atom (IBLCKP). This array was allocated so
far as INTEG4(NATOM) on the heap. However, when IMAGE atoms are
present, the energy routines attempt to find out to which block an
IMAGE atom belongs. This at one point or the other causes a memory
access violation. The solution consists out of two parts. (i) The
IBLCKP data-structure is now allocated as INTEG4(MAXAIM) on the heap;
therefore there is always enough space provided. (ii) The entries for
the IMAGE atoms have to be initialized, and this has to be done at
EVERY image update. However, similar things are already done for a
number of other quantities like masses, vdW params, charges etc. All
this is done among a number of other things in subroutine MKIMAT in
upimag.src, where I have added an appropriate statement.
Ad (2), changes to post-processing routines: Real/Image atoms
leave/enter the simulation box/system dynamically. Therefore, the
nonbonded/image interaction lists have to be updated during
post-processing. The hooks were already in the program, subroutine
BLUPLST. The real changes hide in this routine, most changes in
BLFREE, BLEAVG and BLCOMP are either cosmetic or ensure proper
printout. Post-processing routines FREE, EAVG and COMP will actually
print IMAGE terms if present. The routine BLUPLST is a sibling of
routine updeci in heurist.src. The heuristic update scheme itself is
removed, as I feel that one should update the lists at every frame.
Also, the CRYSTAL specific section of UPDECI is not present in BLUPLST
as I don't understand it. Therefore, care should be exercised when
using BLOCK with CRYSTAL! Negative values of INBFRQ/IMGFRQ are
trapped, in this case they are set to 1; Printout from the update /
list generation routines is suppressed by temporarily raising the
PRNLEV to 1.
The BLOCK documentation (block.doc) has been revised and reflects
these modifications. A new testcase block3.inp has been added to
test/c24test.
[17] Constraint correction for PERT
- Stefan Boresch
The current version of PERT cannot handle situations where SHAKE
is applied to bonds which change in length due to an alchemical
mutation
as SHAKE and PERT do not "communicate". Furthermore, in such cases a
constraint correction has to be computed and added to the free energy
difference. Two steps are required to fix this problem:
(1) The constraint list needs to be updated as a function of the
coupling parameter lambda.
(2) The constraint correction has to be calculated.
Only thermodynamic integration (both for slow-growth and
windowing)
is supported; the exponential formula will give nonsense results. (If
someone wants to fix this, please look at Pearlman/Kollman, JCP 1991,
94, 4532 and Severance et al. J. Comput. Chem. 1995, 16, 311.)
The method to calculate the constraint corrections is based on
extracting the respective Lagrangian multipliers from the SHAKe
routine; this approach is briefly described in van Gunsteren et al.
Computer Simulation of Biomolecular Systems: Theoretical and
Experimental Applications; ESCOM: Leiden 1994; Vol. 2, pp 315-348.
The approach fully includes inertial contributions, it is left to the
user to account for those correctly in the context of the problem.
The new code is mostly transparent and does not really require
additional documentation. However, some information is added to
pert.doc. A new testcase pert2.inp is also added to test/c24test.
[18] Non-Cubic Crystal Building Problem Fix
- Wonpil Im and Ryszard Czerminski
The crystal build facility uses the symmetrized rotated shape matrix
XTLABC obtained from lattice parameters. However, it does not apply
the same rotation to the unit cell moiety, which may result in bad
contacts in non-cubic crystals. The problem is fixed by calling the
subroutine ROTXTL. Some tests for the rotation are added by Ryszard.
Major Enhancements and Developments in CHARMM25
During the C25 development cycle, August 15, 1995 to August 15, 1997,
we made three bugfix-updates in the c24 releases and three alpha versions
and one beta version in the c25 development line.
CHARMM24.0
c24b2 Release February 15, 1996
c24g1 Release August 15, 1996
c24g2 Release February 15, 1997
CHARMM25.0
c25a0 Developmental August 15, 1995
c25a1 Developmental February 15, 1996
c25a2 Developmental August 15, 1996
c25a3 Developmental February 15, 1997
c25b1 Release August 15, 1997
Only bugfixes are incorporated into CHARMM24 and all new developments
and enhancements have been carried out with the CHARMM25 developmental
versions. All modifications are thoroughly recorded in the
ChangeLog.c25 file and the following is the summary of new features
and major enhancements in CHARMM 25.
New Features in CHARMM25
------------------------
[1] Merck Molecular Force Field (MMFF)
- Thomas A. Halgren, Ryszard Czerminski, Jay L. Banks,
Bernard R. Brooks, and Youngdo Won
Merck Molecular Force Field (MMFF) developed by Tom Halgren at
Merck has been implemented in CHARMM. Ryszard introduced MMFF into
c23f2, which made the c24x1 (February 15, 1994) version for evaluation.
As CHARMM was evolved through the c24 development project, Jay
incorporated MMFF into c24b1 in a less intrusive manner. Bernie and
other developers reviewed c24b1/MMFF and suggested some corrections.
Youngdo took the Jay's code and Bernie's suggestions and made the
checkin code of MMFF. MMFF is documented in doc/mmff.doc.
[2] CADPAC
- Paul Lyne
An interface is added to allow CHARMM to run with CADPAC6.0 when
performing QM-MM calculations. CADPAC6.0 can perform HF, MP2, MP3 and DF
calculations.
[3] Particle Mesh Ewald Code
- Bernard R. Brooks
The Particle Mesh Ewald (PME) method has been implemented. This
code is based on code sent by Tom Darden at NIEHS/NIH. It has been
modified so as to conform with CHARMM coding standards. This version
is much faster than the standard Ewald code and accuracy does not appear
to be a problem when reasonable options are used. This code uses the
new "smooth" algorithm. See ewald.doc for more details.
The code is now running in parallel and the following features are
supported:
- PERT (free energy calculation) with PME (including pressures)
- Assymetric units with CRYSTAL (when NOPEr>0 in CRYStal BUILd command)
is now supported with PME.
- Total charge (Qtot<>0) energy and pressure correction term has been added.
- Accurate pressures for the triclinic (and all other) cases (and for PERT)
- Ewald energy components have been separated and can be turned off
with the SKIP command ('EWKS','EWSE','EWEX','EWQC','EWUT').
(k-space,self term,exclusion,total Q correction,utility)
[4] External Force to Selected Atoms
- Lennart Nilsson
A new command has been added which calculates a new energy term
corresponding to a static or periodically varying external force on an atom
selection.
[5] Distance matrix and radius of gyration restraints
- Charles L. Brooks, III, Felix B. Sheinerman and Erik Boczko
New restraint energy terms added to permit restraint of system based
on its radius of gyration and/or the value of a reaction coordiante what
describes the degree of nativeness based on the number of native side
chain contacts. New Keywords are RGYCONS and DMCONS.
[6] HTML Doc Files
- Rick Venable and Charles L. Brooks, III
Added html documentation files and developed/modified doc2html.com
originally developed at NIH. All relevant files added to support/htmldoc
Major Enhancements in CHARMM25
------------------------------
[1] PARALLEL CODE reorganized and extended
- Milan Hodoscek, Charles L. Brooks
The parallel code has been updated and organized into three parts:
paral1.src, paral2.src and paral3.src. The new code is faster and there
has been a significant additions to support other platforms. We now
support about 15 platforms including ALPHAMP, T3D, T3E, Terra,
Global-Works-Server and others.
[2] Linux Port
- Milan Hodoscek
The Linux port is done with the GNU Fortran compiler, version 0.5.18.
For now, all Linux related changes are under the GNU keyword.
[3] Nonbond Energy Code Overhaul with Semi-Automatic Code Expansion
- Bernard R. Brooks
The program PREFLX (PREFX) has been overhauled to allow semi-automatic
code expansion in the moving of inner loop if-tests to the outside of
do-loops. The nonbond energy routines are cleaned and organized to
utilized the semi-automatic expansion. Obsolete ZTBL code is removed.
[4] Ewald code
- Bernard R. Brooks
Memory needs of the EWALD electrostatic option have been reduced,
and multiple parallel options are now supported. Pressure code has been
fixed as well.
The calling sequence to ENBOND was modified so that a flag (QEWEX)
can be sent indicating whether the nonbond exclusion correction should be
performed for the Ewald calculation. This corrects several problems
(such as Ewald with MTS and Ewald with PERT) and this simplifies some code
relative to the handling of the exclusion lists. Also there were several
changes to EPERT so that the Ewald method will report a correct internal
virial (for pressure). The Ewald method was enabled for the GROUP option
so that group lists can be used. This reduces the amount of memory and the
time needed to handle the nonbond lists (good for limited memory parallel
machines).
A version of EWALD was developed for MMFF. The usual MMFF electrostatic
term: qq/(r+d) is split into two terms: qq/r - qq*d/(r*(r+d)) The first
term is handled by the Ewald method in the usual manner (real-space and
k-space parts) and the second term is truncated at the cutoff distance
using a switching function (from CTONNB to CTOFNB). Since the second term
is quite small at the cutoff distance, the use of a switching function
should not introduce significant artificial forces.
[5] Restrained Distance Code Enhancement
- Bernard R. Brooks
The restained distance method has been extended to allow the use of
a one sided function (positive or negative). It also allows a non-unit
exponent for the individual distance terms. The code is now much more
general in its ability to define distnace based retraints based on multiple
distances.
[6] COOR DIPOLE
- Bernard R. Brooks
A COOR DIPOle command has been added. This command computes tha charge
and dipole (multipoles) for selected atoms.
[7] READ PSF APPEnd
- Bernard R. Brooks
The READ PSF APPEnd command option has been modified so that it does
not initialize the coordinates of existing atoms. Only the new appended
atoms will have undefined coordinates.
[8] Replica within Images
- Bernard R. Brooks
The replica code has been enhanced so that it workes with images and the
crystal facility.
[9] The crystal facility has been extended
- Bernard R. Brooks
The follwing new features have been added:
- The "DODE" has been renamed "OCTA" (for truncated OCTAhedron).
(pressure bug fixed for OCTA)
- A new type "RHDO" has been added (for RHombic DOdecahedron).
- The CRYSTAL BUILD command is now much faster and more accurate.
The use of the double atom search has been limited.
- The documentation has been updated to give detailed information
regarding crystal types.
- The WRITe/PRINt IMAGE command is no longer iterative (in accord
with the existing documentation).
[10] Overhaul of Harmonic restraints
- Bernard R. Brooks
The CONS HARM command has been overhauled and extended. The new syntax
has three different types of harmonic restraints:
CONStraint HARMonic { [ABSOlute] absolute-specs } force-const-spec
{ BESTfit coordinate-spec }
{ RELAtive 2nd-atom-selection }
{ CLEAr }
The ABSOlute is the old method. The BESTfit causes the reference set to be
logically bestfit rotated/translated before computing the restraint energy.
The RELAtive allows two portions of one PSF to be restrained to the same
internal geometry by the bestfit least squares rotation (no reference
coordinates used).
Some features and changes:
- Multiple restraints (same or different types) are allowed.
- HARMonic restraint I/O is no longer supported.
- The old command syntax still functions (no rewrite of scripts required).
- The READ/PRINt/WRITe CONS commands now have a "PSF 0" option for PERT.
- PERT supports all of these restraint types.
Restriction:
- Each atom may participate in AT MOST one harmonic restraint term.
[11] Enhancement to REPLICA/PATH
- Bernard R. Brooks
The REPLICA/PATH method has been extended to allow for bestfit translation
and/or rotations between adjacent replicas before computing the restraint
energies. Getting the forces right was the hard part. This allows entire
molecules to be replicated (or sections with significant freedom).
RPATh [ KRMS real ] [ KANGle real ] [ COSMax real ] [MASS] [WEIGht]
[ KMAXrms real ] [RMAXrms real ] [ ROTAtions ] [ TRANslations ]
[12] CHARMM/GAMESS enhanced
- Milan Hodoscek
The version of GAMESS has been updated to the March-97 version
from Ameslab. Also, QM/MM gaussian blur of MM charges has been
implemented as an option.
[13] A few small changes to MMFP and NMR
- Benoit Roux
A few small changes to some MMFP subroutine have been made. The
main thing is a second atom select for the SSBP command that allows
the present of atoms outside the boundary radius. This could be
useful when the boundary is used only for an active site. The
relaxation time due to the chemical shift anisotropy addition has
been added to NMR.
[14] COOR DMAT
- Charles L. Brooks, III
The dist keyword has been removed from the covariance command and
a new analysis command has been added under the coor subsyntax. This
command is accessed with the command COOR DMAT and provides some
general tools for the calculation, manipulation and storage/extraction
of distance matrix based properties. This routine has some overlap
with the new distance command introduced by Bernie Brooks but also
provides significant complementarity in extending the range of
properties computed.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute